[gmx-users] crystals of KCl during simulation

[Marc Baaden]

Hi,

regafan at hotmail.com said:
>> [..] but after equilibration I have observed that KCl is aggregating, like
>> if it was making crystals. When I used NaCl instead KCl, this not
>> happened.

>> Does anybody has any idea about the reason of the behaviour of KCl in
>> the simulation?

This even does happen with Amber :)  So my guess is you correctly transferred
the parameters, but stumbled upon an artefact. If you check the recent 
literature you may notice that many publications with Amber using K+ 
only employ minimal (neutralising) salt conditions as a workaround. At 
least this is what we did recently [1].

Marc Baaden

[1] Interactions between neuronal fusion proteins explored by molecular
dynamics, Biophys.J.94, 2008, 3436-3446.
http://dx.doi.org/10.1529/biophysj.107.123117

-- 
 Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
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